I am looking at using QIIME to compare biomes, but finding it difficult to get started as I am not used to command line driven programs. Is their a good beginners guide on the net somewhere, or perhaps an easier to use alternative?
Thanks Nsa, looks like I am going to upgrade my Linux skills!
Hi Jerry,
I was in a similar situation like your. Get into any Ubuntu forum (mentioned in first point below) and learn the basics of navigation within linux file system. You don't have to install Ubuntu separately. You can use the learning process within Qiime software, as its a virtual Ubuntu OS with qiime installed. Just install oracle virtual box software, download the qiime software and mount it on the virtual box software. Rest is easy to follow from the Qiime webpage if you get the linux basic command. No more than basics is required.
1. http://ryanstutorials.net/linuxtutorial/ (i recommend using this blog to learn linux basic commands)
2. http://www.virtualbox.org/wiki/Downloads (download oracle virtual box and install in your windows or mac system)
3. ftp://thebeast.colorado.edu/pub/qiime-release-VMs/QIIME-1.8.0-amd64.vdi.gz (download this 64 bit qiime software and extract and save it. Note: qiime is not supported for 32 bit system and this software is a large file so you need a high speed internet for less time, or use a software called Filezilla (ftp client) paste the above ftp link provide and start downloading, you can resume your download if it fails in between)
One you have done done step two and three, go the following youtube video link and do as directed.
4. http://youtu.be/1jYupkquaME (youtube link for configuring qiime software on windows or mac system)
5. http://qiime.org/tutorials/tutorial.html (use this qiime tutorial to work with either 454 or illumina generated reads.)
However if you want to go for an alternative. Use MG-RAST which is GUI based and easy to follow. You can analyze your *.biom files there as well.
Qiime has an advantage of working offline at your leisure whereas in MG RAST you have to analyze data online. In qiime you get to learn about the entire process of analysis.
you can also get step by step command and example here
https://github.com/alexcritschristoph/Qiime16sTutorial
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